BioStructures API

Read, write and manipulate macromolecular structures.

An atom that is part of a macromolecule - either an Atom or a DisorderedAtom.

A residue (amino acid) or other molecule - either a Residue or a DisorderedResidue.

An atom that is part of a macromolecule.

A record for a single atom, e.g. as represented in a Protein Data Bank (PDB) file.

A chain (molecule) from a macromolecular structure.

ContactMap(element, contact_distance)
ContactMap(element_one, element_two, contact_distance)
ContactMap(bit_array_2D)

Calculate the contact map for a StructuralElementOrList, or between two StructuralElementOrLists.

This returns a ContactMap type containing a BitArray{2} with true where the sub-elements are no further than the contact distance and false otherwise. When one element is given as input this returns a symmetric square matrix. To directly access the underlying data of ContactMap cm, use cm.data.

Examples

cbetas_A = collectatoms(struc["A"], cbetaselector)
cbetas_B = collectatoms(struc["B"], cbetaselector)

# Contact map of chain A using conventional Cβ and 8 Å definitions
cm = ContactMap(cbetas_A, 8.0)

# Returns true if a contact is present between the tenth and twentieth element
cm[10, 20]

# Rectangular contact map of chains A and B
cm = ContactMap(cbetas_A, cbetas_B, 8.0)

# Write the contact map to file
using DelimitedFiles
writedlm("contacts.out", Int64.(cm.data), " ")

A container to hold different locations of the same atom.

A container to hold different versions of the same residue (point mutations).

DistanceMap(element)
DistanceMap(element_one, element_two)
DistanceMap(float_array_2D)

Calculate the distance map for a StructuralElementOrList, or between two StructuralElementOrLists.

This returns a DistanceMap type containing a Array{Float64, 2} with minimum distances between the sub-elements. When one element is given as input this returns a symmetric square matrix. To directly access the underlying data of DistanceMap dm, use dm.data.

Examples

cbetas_A = collectatoms(struc["A"], cbetaselector)
cbetas_B = collectatoms(struc["B"], cbetaselector)

# Distance map of chain A showing how far each Cβ atom is from the others
dm = DistanceMap(cbetas_A)

# Returns the distance between the tenth and twentieth element
dm[10, 20]

# Rectangular distance map of chains A and B
dm = DistanceMap(cbetas_A, cbetas_B)

# Write the distance map to file
using DelimitedFiles
writedlm("distances.out", dm.data, " ")

MMCIFDict(filepath; gzip=false)
MMCIFDict(io; gzip=false)
MMCIFDict()

A macromolecular Crystallographic Information File (mmCIF) dictionary.

Can be accessed using similar functions to a standard Dict. Keys are field names as a String and values are always Vector{String}, even for multiple components or numerical data. To directly access the underlying dictionary of MMCIFDict d, use d.dict. Call MMCIFDict with a filepath or stream to read the dictionary from that source. The keyword argument gzip (default false) determines if the input is gzipped.

Protein Data Bank (PDB) mmCIF file format.

MMTFDict(filepath; gzip=false)
MMTFDict(io; gzip=false)
MMTFDict()

A Macromolecular Transmission Format (MMTF) dictionary.

Use of the dictionary requires the MMTF.jl package to be imported. Can be accessed using similar functions to a standard Dict. Keys are field names as a String and values are various types. To directly access the underlying dictionary of MMTFDict d, use d.dict. Call MMTFDict with a filepath or stream to read the dictionary from that source. The keyword argument gzip (default false) determines if the file is gzipped.

Protein Data Bank (PDB) MMTF file format.

A conformation of a macromolecular structure.

A container for multiple Models that represents a Protein Data Bank (PDB) entry.

Error arising from an attempt to make an inconsistent structural state.

Protein Data Bank (PDB) file format.

Error arising from parsing a Protein Data Bank (PDB) file.

Protein Data Bank (PDB) XML file format.

A residue (amino acid) or other molecule.

A map of a structural property, e.g. a ContactMap or a DistanceMap.

A macromolecular structural element.

Transformation(el1, el2, residue_selectors...)
Transformation(coords1, coords2)
Transformation(trans1, trans2, rot)

A 3D transformation to map one set of coordinates onto another, found using the Kabsch algorithm.

When called with structural elements, carries out a pairwise alignment and superimposes on atoms from aligned residues. In this case the BioSequences.jl and BioAlignments.jl packages should be imported. Keyword arguments for pairwise alignment can be given, see pairalign. The residue selectors determine which residues to do the pairwise alignment on. The keyword argument alignatoms is an atom selector that selects the atoms to calculate the superimposition on (default calphaselector). Can also be called with two sets of coordinates of the same size, with the number of dimensions in the first axis and the number of points in the second axis.

The returned Transformation object consists of the mean coordinates of the first set, the mean coordinates of the second set, the rotation to map the first centred set onto the second centred set, and the indices of the aligned residues in the first and second elements if relevant.

A StructuralElement or Vector of StructuralElements up to a Vector{Model}.

Set of protein backbone atom names.

Set of Cα atom names.

Set of Cβ atom names.

Set of secondary structure codes corresponding to a coil.

Set of secondary structure codes corresponding to an α-helix.

Mapping of Protein Data Bank (PDB) formats to their file extensions.

Set of residue names found in proteins and peptides.

Set of secondary structure codes corresponding to a β-sheet.

Lookup table of amino acids, re-exported from BioSymbols.

Set of residue names corresponding to water.

collect(el)

Returns a Vector of the sub-elements in a StructuralElementOrList, e.g. AbstractAtoms in a Residue or AbstractResidues in a Chain.

read(filepath::AbstractString, format::Type; <keyword arguments>)
read(input::IO, format::Type; <keyword arguments>)

Read a Protein Data Bank (PDB) file and return a MolecularStructure.

Arguments

• format::Type: the format of the PDB file; options are PDBFormat, MMCIFFormat and MMTFFormat. MMTFFormat requires the MMTF.jl package to be imported.
• structure_name::AbstractString: the name given to the returned MolecularStructure; defaults to the file name.
• remove_disorder::Bool=false: whether to remove atoms with alt loc ID not ' ' or 'A'.
• read_std_atoms::Bool=true: whether to read standard ATOM records.
• read_het_atoms::Bool=true: whether to read HETATOM records.
• run_dssp::Bool=false: whether to run DSSP to assign secondary structure. Requires the DSSP_jll.jl package to be imported if set to true.
• run_stride::Bool=false: whether to run STRIDE to assign secondary structure. Requires the STRIDE_jll.jl package to be imported if set to true.
• gzip::Bool=false: whether the input is gzipped, not available for PDB format.

distance(element_one, element_two, atom_selectors...)

Get the minimum distance in Å between two StructuralElementOrLists.

Additional arguments are atom selector functions - only atoms that return true from the functions are retained.

acidicresselector(res)
acidicresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, an acidic amino acid based on the residue name.

aliphaticresselector(res)
aliphaticresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, an aliphatic amino acid based on the residue name.

allselector(at)
allselector(res)

Trivial selector that returns true for any structural element.

altlocid(at)

Get the alternative location ID of an AbstractAtom as a Char.

altlocids(dis_at)

Get the list of alternative location IDs in an AbstractAtom as a Vector{Char}, sorted by atom serial.

applyselectors!(els, selectors...)

Removes from a Vector of StructuralElements all elements that do not return true from all the selector functions.

applyselectors(els, selectors...)

Returns a copy of a Vector of StructuralElements with all elements that do not return true from all the selector functions removed.

applytransform!(el, transformation)

Modify all coordinates in an element according to a transformation.

applytransform(coords, transformation)

Modify coordinates according to a transformation.

aromaticresselector(res)
aromaticresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, an aromatic amino acid based on the residue name.

atomid(at)

Get a descriptive atom ID for an AbstractAtom as a Tuple of the form (full residue ID, residue name, atom name).

atomname(at; strip=true)

Get the atom name of an AbstractAtom as a String. strip determines whether surrounding whitespace is stripped.

atomnames(res; strip=true)

Get the sorted list of AbstractAtoms in an AbstractResidue. strip determines whether surrounding whitespace is stripped.

atomnameselector(at, atom_names; strip=true)

Determines if an AbstractAtom has its atom name in a list of names. strip determines whether surrounding whitespace is stripped from the atom name before it is checked in the list.

atoms(res)

Return the dictionary of AbstractAtoms in an AbstractResidue.

backboneselector(at)

Determines if an AbstractAtom is not a hetero-atom and corresponds to a protein backbone atom.

basicresselector(res)
basicresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, a basic amino acid based on the residue name.

bondangle(atom_a, atom_b, atom_c)
bondangle(vec_ba, vec_bc)

Calculate the bond or pseudo-bond angle in radians between three AbstractAtoms or two vectors.

The angle between B→A and B→C is returned in the range 0 to π.

calphaselector(at)

Determines if an AbstractAtom is not a hetero-atom and corresponds to a Cα atom.

cbetaselector(at)

Determines if an AbstractAtom is not a hetero-atom and corresponds to a Cβ atom, or a Cα atom in glycine.

chain(at)
chain(res)

Return the Chain that an AbstractAtom or AbstractResidue belongs to.

chainid!(ch, id)
chainid!(res, id)

Set the chain ID of a Chain or an AbstractResidue to a new String.

If a chain with this ID already exists, it will be removed from its current chain and added to that chain. If a chain with this ID does not exist, a new chain will be added to the model and this residue will be added to it. If moving this residue from a chain to a new chain leaves the old chain without residues, the old chain will be removed from the Model.

chainid(el)

Get the chain ID of an AbstractAtom, AbstractResidue or Chain as a String.

chainids(model)
chainids(struc)

Get the sorted chain IDs of the chains in a Model, or the default Model of a MolecularStructure, as a Vector{String}.

chains(model)
chains(struc)

Return the dictionary of Chains in a Model, or the default Model of a MolecularStructure.

charge(at; strip=true)

Get the charge on an AbstractAtom as a String. The charge is set to " " if not specified during atom creation. strip determines whether surrounding whitespace is stripped.

chargedresselector(res)
chargedresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, a charged amino acid based on the residue name.

chiangle(res, i)

Calculate the χᵢ angle in radians for a standard AbstractResidue with standard atom names. The angle is in the range -π to π.

chiangles(res)

Calculate the Vector of standard χ angles for a standard AbstractResidue with standard atom names. The length of the vector ranges from 0 (GLY, ALA) to 5 (ARG). The angles are each in the range -π to π.

chiangles(element, residue_selectors...)

Calculate the Vector of standard χ angles for each residue in a StructuralElementOrList. This returns a Vector of Vectors, where all angles are in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

choosedefaultaltlocid(at_one, at_two)

Determine which of two Atoms representing a disorered atom better qualifies as the default location.

The Atom with the highest occupancy is chosen; in the case of ties the Atom with the lowest alternative location ID in alphabetical order is chosen.

coilselector(res)
coilselector(at)

Determines if an AbstractResidue or AbstractAtom is part of a coil, i.e. whether the secondary structure code is in coilsscodes.

collectatoms(el)

Returns a Vector of the atoms in a StructuralElementOrList.

Additional arguments are atom selector functions - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default false) determines whether to return all copies of disordered atoms separately.

collectchains(el)

Returns a Vector of the chains in a StructuralElementOrList.

Additional arguments are chain selector functions - only chains that return true from all the functions are retained.

collectmodels(el)

Returns a Vector of the models in a StructuralElementOrList.

Additional arguments are model selector functions - only models that return true from all the functions are retained.

collectresidues(el)

Returns a Vector of the residues in a StructuralElementOrList.

Additional arguments are residue selector functions - only residues that return true from all the functions are retained. The keyword argument expand_disordered (default false) determines whether to return all copies of disordered residues separately.

coordarray(element, atom_selectors...)

Get the atomic coordinates in Å of a StructuralElementOrList as a 2D Array.

Each column corresponds to one atom, so the size is (3, natoms). Additional arguments are atom selector functions - only atoms that return true from all the functions are retained. The keyword argument `expanddisordered(defaultfalse`) determines whether to return coordinates for all copies of disordered atoms separately.

coords!(at, new_coords)

Set the coordinates in Å of an AbstractAtom to a Vector of 3 numbers.

For DisorderedAtoms only the default atom is updated.

coords(at)

Get the coordinates in Å of an AbstractAtom as a Vector{Float64}.

countatoms(el)

Return the number of atoms in a StructuralElementOrList as an Int.

Additional arguments are atom selector functions - only atoms that return true from all the functions are counted. The keyword argument expand_disordered (default false) determines whether to return all copies of disordered atoms separately.

countchains(el)

Return the number of Chains in a StructuralElementOrList as an Int.

Additional arguments are chain selector functions - only chains that return true from all the functions are counted.

countmodels(el)

Return the number of Models in a StructuralElementOrList as an Int.

Additional arguments are model selector functions - only models that return true from all the functions are counted.

countresidues(el)

Return the number of residues in a StructuralElementOrList as an Int.

Additional arguments are residue selector functions - only residues that return true from all the functions are counted. The keyword argument expand_disordered (default false) determines whether to return all copies of disordered residues separately.

defaultaltlocid(dis_at)

Get the alternative location ID of the default Atom in a DisorderedAtom as a Char.

The default is the highest occupancy, or lowest character alternative location ID for ties (i.e. 'A' beats 'B').

defaultatom(dis_at)

Return the default Atom in a DisorderedAtom.

The default is the highest occupancy, or lowest character alternative location ID for ties (i.e. 'A' beats 'B').

defaultmodel(struc)

Get the default Model in a MolecularStructure.

This is the Model with the lowest model number.

defaultresidue(dis_res)

Return the default Residue in a DisorderedResidue.

The default is the first name read in.

defaultresname(dis_res)

Get the name of the default Residue in a DisorderedResidue as a String.

The default is the first name read in.

dihedralangle(atom_a, atom_b, atom_c, atom_d)
dihedralangle(vec_ab, vec_bc, vec_cd)

Calculate the dihedral angle in radians defined by four AbstractAtoms or three vectors.

The angle between the planes defined by atoms (A, B, C) and (B, C, D) is returned in the range -π to π.

disorderedres(dis_res, res_name)

Return the Residue in a DisorderedResidue with a given residue name.

disorderselector(at)
disorderselector(res)

Determines whether an AbstractAtom or AbstractResidue is disordered, i.e. has multiple locations in the case of atoms or multiple residue names (point mutants) in the case of residues.

displacements(element_one, element_two, residue_selectors...)
displacements(element_one, element_two, superimpose=false)
displacements(coords_one, coords_two)

Get the displacements in Å between atomic coordinates from two StructuralElementOrLists or two coordinate Arrays.

If superimpose is true (the default), the elements are superimposed before calculation and the displacements are calculated on the superimposed residues. In this case the BioSequences.jl and BioAlignments.jl packages should be imported. See Transformation for keyword arguments. If superimpose is false the elements are assumed to be superimposed and must be of the same length. The keyword argument dispatoms is an atom selector that selects the atoms to calculate displacements on (default calphaselector).

downloadallobsoletepdb(; <keyword arguments>)

Download all obsolete Protein Data Bank (PDB) files from the RCSB server.

Returns the list of PDB IDs downloaded. Requires an internet connection.

Arguments

• obsolete_dir::AbstractString=pwd(): the directory where the PDB files are downloaded; defaults to the current working directory.
• format::Type=PDBFormat: the format of the PDB file; options are PDBFormat, PDBXMLFormat and MMCIFFormat. MMTF files are no longer available to download.
• overwrite::Bool=false: if set true, overwrites the PDB file if it exists in dir; by default skips downloading the PDB file if it exists.

downloadentirepdb(; <keyword arguments>)

Download the entire Protein Data Bank (PDB) from the RCSB server.

Returns the list of PDB IDs downloaded. Ensure you have enough disk space and time before running. The function can be stopped any time and called again to resume downloading. Requires an internet connection.

Arguments

• dir::AbstractString=pwd(): the directory to which the PDB files are downloaded; defaults to the current working directory.
• format::Type=PDBFormat: the format of the PDB file; options are PDBFormat, PDBXMLFormat and MMCIFFormat. MMTF files are no longer available to download.
• overwrite::Bool=false: if set true, overwrites the PDB file if it exists in dir; by default skips downloading the PDB file if it exists.

downloadpdb(pdbid::AbstractString; <keyword arguments>)
downloadpdb(pdbid::AbstractArray{<:AbstractString, 1}; <keyword arguments>)
downloadpdb(f::Function, args...)

Download files from the Protein Data Bank (PDB) via RCSB.

When given an AbstractString, e.g. "1AKE", downloads the PDB file and returns the path to the file. When given an Array{<:AbstractString, 1}, downloads the PDB files in the array and returns an array of the paths to the files. When given a function as the first argument, runs the function with the downloaded filepath(s) as an argument then removes the file(s). Requires an internet connection.

Arguments

• dir::AbstractString=pwd(): the directory to which the PDB file is downloaded; defaults to the current working directory.
• format::Type=PDBFormat: the format of the PDB file; options are PDBFormat, PDBXMLFormat and MMCIFFormat. MMTF files are no longer available to download.
• obsolete::Bool=false: if set true, the PDB file is downloaded in the auto-generated "obsolete" directory inside the specified dir.
• overwrite::Bool=false: if set true, overwrites the PDB file if it exists in dir; by default skips downloading the PDB file if it exists.
• ba_number::Integer=0: if set > 0 downloads the respective biological assembly; by default downloads the PDB file.

element(at; strip=true)

Get the element of an AbstractAtom as a String.

The element is set to " " if not specified during atom creation. strip determines whether surrounding whitespace is stripped.

generatechainid(entity_id)

Convert a positive Integer into a chain ID.

Goes A to Z, then AA to ZA, AB to ZB etc. This is in line with Protein Data Bank (PDB) conventions.

heavyatomselector(at)

Determines if an AbstractAtom corresponds to a heavy (non-hydrogen) atom and is not a hetero-atom.

helixselector(res)
helixselector(at)

Determines if an AbstractResidue or AbstractAtom is part of an α-helix, i.e. whether the secondary structure code is in helixsscodes.

heteroselector(at)
heteroselector(res)

Determines if an AbstractAtom represents a hetero atom, e.g. came from a HETATM record in a Protein Data Bank (PDB) file, or if an AbstractResidue represents a hetero molecule, e.g. consists of HETATM records from a PDB file.

hydrogenselector(at)

Determines if an AbstractAtom represents hydrogen.

Uses the element field where possible, otherwise uses the atom name.

hydrophobicresselector(res)
hydrophobicresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, a hydrophobic amino acid based on the residue name.

inscode(at)
inscode(res)

Get the insertion code of an AbstractAtom or AbstractResidue as a Char.

isdisorderedatom(at)

Determines if an AbstractAtom is a DisorderedAtom, i.e. if there are multiple locations present for an atom.

isdisorderedres(res)

Determine if an AbstractResidue is a DisorderedResidue, i.e. there are multiple residue names with the same residue ID.

ishetero(at)
ishetero(res)

Determines if an AbstractAtom represents a hetero atom, e.g. came from a HETATM record in a Protein Data Bank (PDB) file, or if an AbstractResidue represents a hetero molecule, e.g. consists of HETATM records from a PDB file.

model(el)

Return the Model that an AbstractAtom, AbstractResidue or Chain belongs to.

modelnumber(el)

Get the model number of a Model, Chain, AbstractResidue or AbstractAtom as an Int.

modelnumbers(struc)

Get the sorted model numbers from a MolecularStructure as a Vector{Int}.

models(struc)

Return the dictionary of Models in a MolecularStructure.

neutralresselector(res)
neutralresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, a neutral amino acid based on the residue name.

nonpolarresselector(res)
nonpolarresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, a non-polar amino acid based on the residue name.

notwaterselector(res)
notwaterselector(at)

Determines if an AbstractResidue or AbstractAtom does not represent a water molecule, i.e. whether the residue name is not in waterresnames.

occupancy(at)

Get the occupancy of an AbstractAtom as a Float64.

The occupancy is set to 1.0 if not specified during atom creation.

omegaangle(res, res_previous)
omegaangle(chain, res_id)

Calculate the omega angle in radians for an AbstractResidue.

Arguments can either be a residue and the previous residue or a chain and the position as a residue ID. The first residue (or one at the given index) requires the atoms "N" and "CA" and the previous residue requires the atoms "CA" and "C". The angle is in the range -π to π.

omegaangles(element, residue_selectors...)

Calculate the Vector of omega angles of a StructuralElementOrList.

The vectors have NaN for residues where an angle cannot be calculated, e.g. due to missing atoms or lack of an adjacent residue. The angle is in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

pdbentrylist()

Obtain the list of all Protein Data Bank (PDB) entries from the RCSB server.

Requires an internet connection.

pdbline(at::Atom)
pdbline(at::DisorderedAtom)
pdbline(at::AtomRecord)

Form a Protein Data Bank (PDB) format ATOM or HETATM record as a String from an Atom, DisorderedAtom or AtomRecord.

This will throw an ArgumentError if a value cannot fit into the allocated space, e.g. the chain ID is longer than one character or the atom serial is greater than 99999. In this case consider using writemmcif or writemmtf to write a mmCIF file or a MMTF file.

pdbobsoletelist()

Obtain the list of all obsolete Protein Data Bank (PDB) entries from the RCSB server.

Requires an internet connection.

pdbrecentchanges()

Obtain three lists giving the added, modified and obsolete Protein Data Bank (PDB) entries from the recent RCSB weekly status files.

Requires an internet connection.

pdbstatuslist(url::AbstractString)

Obtain the list of Protein Data Bank (PDB) entries from a RCSB weekly status file by specifying its URL.

An example URL is https://files.wwpdb.org/pub/pdb/pub/pdb/data/status/latest/added.pdb. Requires an internet connection.

phiangle(res, res_previous)
phiangle(chain, res_id)

Calculate the phi angle in radians for an AbstractResidue.

Arguments can either be a residue and the previous residue or a chain and the position as a residue ID. The first residue (or one at the given index) requires the atoms "N", "CA" and "C" and the previous residue requires the atom "C". The angle is in the range -π to π.

phiangles(element, residue_selectors...)

Calculate the Vector of phi angles of a StructuralElementOrList.

The vectors have NaN for residues where an angle cannot be calculated, e.g. due to missing atoms or lack of an adjacent residue. The angle is in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

polarresselector(res)
polarresselector(at)

Determines if an AbstractResidue is, or an AbstractAtom is part of, a polar amino acid based on the residue name.

proteinselector(res)
proteinselector(at)

Determines if an AbstractResidue or AbstractAtom is part of a protein or peptide based on the residue name.

psiangle(res, res_next)
psiangle(chain, res_id)

Calculate the psi angle in radians for an AbstractResidue.

Arguments can either be a residue and the next residue or a chain and the position as a residue ID. The first residue (or one at the given index) requires the atoms "N", "CA" and "C" and the next residue requires the atom "N". The angle is in the range -π to π.

psiangles(element, residue_selectors...)

Calculate the Vector of psi angles of a StructuralElementOrList.

The vectors have NaN for residues where an angle cannot be calculated, e.g. due to missing atoms or lack of an adjacent residue. The angle is in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

ramachandranangles(element, residue_selectors...)

Calculate the Vectors of phi and psi angles of a StructuralElementOrList.

The vectors have NaN for residues where an angle cannot be calculated, e.g. due to missing atoms or lack of an adjacent residue. The angles are in the range -π to π. Additional arguments are residue selector functions - only residues that return true from the functions are retained.

readmultimmcif(filepath; gzip=false)
readmultimmcif(io; gzip=false)

Read multiple MMCIFDicts from a filepath or stream. Each MMCIFDict in the returned Dict{String, MMCIFDict} corresponds to an mmCIF data block from the input. An example of such a file is the chemical component dictionary from the Protein Data Bank. The keyword argument gzip (default false) determines if the input is gzipped.

resid(res; full=true)

Get a descriptive residue ID String for an AbstractAtom or AbstractResidue.

Format is residue number then insertion code with "H" in front for hetero residues. If full equals true the chain ID is also added after a colon. Examples are "50A", "H20" and "10:A".

resids(ch)

Get the sorted list of AbstractResidues in a Chain.

residue(at)

Get the Residue that an AbstractAtom belongs to.

residues(ch)

Return the dictionary of AbstractResidues in a Chain.

resname(at; strip=true)
resname(res; strip=true)

Get the residue name of an AbstractAtom or AbstractResidue as a String.

strip determines whether surrounding whitespace is stripped.

resnames(dis_res)

Get the residue names in an AbstractResidue as a Vector{String}.

For a DisorderedResidue there will be multiple residue names - in this case the default residue name is placed first, then the others are ordered alphabetically.

resnameselector(res, res_names)
resnameselector(at, res_names)

Determines if an AbstractResidue or AbstractAtom has its residue name in a list of names.

resnumber(at)
resnumber(res)

Get the residue number of an AbstractAtom or AbstractResidue as an Int.

retrievepdb(pdbid::AbstractString; <keyword arguments>)

Download and read a Protein Data Bank (PDB) file or biological assembly from the RCSB server, returning a MolecularStructure.

Requires an internet connection.

Arguments

• pdbid::AbstractString: the PDB ID to be downloaded and read.
• dir::AbstractString=pwd(): the directory to which the PDB file is downloaded; defaults to the current working directory.
• format::Type=MMCIFFormat: the format of the PDB file; options are PDBFormat, PDBXMLFormat and MMCIFFormat. MMTF files are no longer available to download.
• obsolete::Bool=false: if set true, the PDB file is downloaded in the auto-generated "obsolete" directory inside the specified dir.
• overwrite::Bool=false: if set true, overwrites the PDB file if it exists in dir; by default skips downloading the PDB file if it exists.
• ba_number::Integer=0: if set > 0 downloads the respective biological assembly; by default downloads the PDB file.
• structure_name::AbstractString="$pdbid.pdb": the name given to the returned MolecularStructure; defaults to the PDB ID.
• remove_disorder::Bool=false: whether to remove atoms with alt loc ID not ' ' or 'A'.
• read_std_atoms::Bool=true: whether to read standard ATOM records.
• read_het_atoms::Bool=true: whether to read HETATOM records.
• run_dssp::Bool=false: whether to run DSSP to assign secondary structure. Requires the DSSP_jll.jl package to be imported if set to true.
• run_stride::Bool=false: whether to run STRIDE to assign secondary structure. Requires the STRIDE_jll.jl package to be imported if set to true.

rmsd(element_one, element_two, residue_selectors...)
rmsd(element_one, element_two, superimpose=false)
rmsd(coords_one, coords_two)

Get the root-mean-square deviation (RMSD) in Å between two StructuralElementOrLists or two coordinate Arrays.

If superimpose is true (the default), the elements are superimposed before RMSD calculation and the RMSD is calculated on the superimposed residues. In this case the BioSequences.jl and BioAlignments.jl packages should be imported. See Transformation for keyword arguments. If superimpose is false the elements are assumed to be superimposed and must be of the same length. The keyword argument rmsdatoms is an atom selector that selects the atoms to calculate RMSD on (default calphaselector).

rundssp(struc)
rundssp(model)
rundssp(filepath_in, dssp_filepath_out)

Return a copy of the structural element with DSSP (Define Secondary Structure of Proteins) run to assign secondary structure, or run DSSP directly on a PDB or mmCIF file.

Requires the DSSP_jll.jl package to be imported.

rundssp!(struc)
rundssp!(model)

Run DSSP (Define Secondary Structure of Proteins) on the given structural element to assign secondary structure.

Requires the DSSP_jll.jl package to be imported. A temporary PDB file is written, so this will fail if the structural element cannot be written to a PDB file, for example if there are two-letter chain IDs.

runstride(struc)
runstride(model)
runstride(filepath_in, stride_filepath_out)

Return a copy of the structural element with STRIDE run to assign secondary structure, or run STRIDE directly on a PDB file.

Requires the STRIDE_jll.jl package to be imported.

runstride!(struc)
runstride!(model)

Run STRIDE on the given structural element to assign secondary structure.

Requires the STRIDE_jll.jl package to be imported. A temporary PDB file is written, so this will fail if the structural element cannot be written to a PDB file, for example if there are two-letter chain IDs.

sequentialresidues(res_first, res_second)

Determine if the second residue follows the first in sequence.

For this to be true the residues need to have the same chain ID, both need to be standard/hetero residues and the residue number of the second needs to be one greater than that of the first (or the residue numbers the same and the insertion code of the second greater than the first).

serial(at)

Get the serial number of an AbstractAtom as an Int.

sheetselector(res)
sheetselector(at)

Determines if an AbstractResidue or AbstractAtom is part of a β-sheet, i.e. whether the secondary structure code is in sheetsscodes.

showcontactmap(contact_map)
showcontactmap(io, contact_map)

Print a representation of a ContactMap to stdout, or a specified IO instance.

A fully plotted version can be obtained with plot(contact_map) but that requires Plots.jl; showcontactmap works without that dependency.

sidechainselector(at)

Determines if an AbstractAtom is not a hetero-atom and corresponds to a protein side chain atom.

spaceatomname(at::Atom)

Space an Atom name such that the last element letter (generally) appears in the second column.

If the element property of the Atom is set it is used to get the element, otherwise the name starts from the second column where possible. This function is generally not required as spacing is recorded when atom names are read in from a Protein Data Bank (PDB) file. However this spacing can be important, for example distinguising between Cα and calcium atoms.

specializeresnames!(el)

Rename residues to reflect the bonding topology.

Renames histidine residues to reflect a specific protonation configuration (HID, HIE, or HIP) based on the presence of HD1 and HE2 atoms. Renames N-terminal and C-terminal (e.g. ALA -> NALA) residues based on the presence of certain atoms. Other residues remain unchanged.

Hydrogens must have been assigned prior to calling this function.

sqdistance(element_one, element_two, atom_selectors...)

Get the minimum square distance in Å between two StructuralElementOrLists.

Additional arguments are atom selector functions - only atoms that return true from the functions are retained.

sscode!(res, ss_code)

Set the secondary structure code of an AbstractResidue to a Char.

sscode(res)
sscode(at)

Get the secondary structure code of an AbstractResidue or AbstractAtom as a Char.

'-' represents unassigned secondary structure. Secondary structure can be assigned using rundssp! or runstride!.

sscodeselector(res, ss_codes)
sscodeselector(at, ss_codes)

Determines if an AbstractResidue or AbstractAtom has its secondary structure code in a list of secondary structure codes.

standardselector(at)
standardselector(res)

Determines if an AbstractAtom represents a standard atom, e.g. came from a ATOM record in a Protein Data Bank (PDB) file, or if an AbstractResidue represents a standard molecule, e.g. consists of ATOM records from a PDB file.

structure(el)

Return the MolecularStructure that an AbstractAtom, AbstractResidue, Chain or Model belongs to.

structurename(el)

Get the name of the MolecularStructure that a StructuralElement belongs to as a String.

superimpose!(el1, el2, residue_selectors...)

Calculate the Transformation that maps the first element onto the second, and modify all coordinates in the first element according to the transformation.

Requires the BioSequences.jl and BioAlignments.jl packages to be imported. See Transformation for keyword arguments.

tempfactor(at)

Get the temperature factor of an AbstractAtom as a Float64.

The temperature factor is set to 0.0 if not specified during atom creation.

updatelocalpdb(; dir::AbstractString=pwd(), format::Type=PDBFormat)

Update a local copy of the Protein Data Bank (PDB).

Obtains the recent weekly lists of new, modified and obsolete PDB entries and automatically updates the PDB files of the given format inside the local dir directory. Requires an internet connection.

waterselector(res)
waterselector(at)

Determines if an AbstractResidue or AbstractAtom represents a water molecule, i.e. whether the residue name is in waterresnames.

writemmcif(output, element, atom_selectors...; gzip=false)
writemmcif(output, mmcif_dict; gzip=false)

Write a StructuralElementOrList or a MMCIFDict to a mmCIF format file or output stream.

Atom selector functions can be given as additional arguments - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default true) determines whether to return all copies of disordered residues and atoms. The keyword argument gzip (default false) determines if the output is gzipped.

writemmtf(output, element, atom_selectors...; gzip=false)
writemmtf(output, mmtf_dict; gzip=false)

Write a StructuralElementOrList or a MMTFDict to a MMTF file or output stream.

Requires the MMTF.jl package to be imported. Atom selector functions can be given as additional arguments - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default true) determines whether to return all copies of disordered residues and atoms. The keyword argument gzip (default false) determines if the file should be gzipped.

writemultimmcif(filepath, cifs; gzip=false)
writemultimmcif(io, cifs; gzip=false)

Write multiple MMCIFDicts as a Dict{String, MMCIFDict} to a filepath or stream. The keyword argument gzip (default false) determines if the output is gzipped.

writepdb(output, element, atom_selectors...)

Write a StructuralElementOrList to a Protein Data Bank (PDB) format file or output stream.

Only ATOM, HETATM, MODEL and ENDMDL records are written - there is no header and there are no TER records. Atom selector functions can be given as additional arguments - only atoms that return true from all the functions are retained. The keyword argument expand_disordered (default true) determines whether to return all copies of disordered residues and atoms.

String selection syntax.

x(at)

Get the x coordinate in Å of an AbstractAtom as a Float64.

x!(at, val)

Set the x coordinate in Å of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.

y(at)

Get the y coordinate in Å of an AbstractAtom as a Float64.

y!(at, val)

Set the y coordinate in Å of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.

z(at)

Get the z coordinate in Å of an AbstractAtom as a Float64.

z!(at, val)

Set the z coordinate in Å of an AbstractAtom to val.

For DisorderedAtoms only the default atom is updated.